Multiple sequence alignment - TraesCS2D01G088500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G088500 chr2D 100.000 4458 0 0 1 4458 38253849 38249392 0.000000e+00 8233.0
1 TraesCS2D01G088500 chr2D 81.242 2367 353 54 1186 3521 38218610 38216304 0.000000e+00 1827.0
2 TraesCS2D01G088500 chr2D 81.054 2106 334 41 1079 3158 38442077 38440011 0.000000e+00 1618.0
3 TraesCS2D01G088500 chr2D 89.663 832 53 14 974 1802 38236067 38235266 0.000000e+00 1029.0
4 TraesCS2D01G088500 chr2D 88.551 856 65 12 3490 4343 38242460 38241636 0.000000e+00 1007.0
5 TraesCS2D01G088500 chr2D 88.831 573 51 7 3835 4401 38549047 38548482 0.000000e+00 691.0
6 TraesCS2D01G088500 chr2D 89.435 407 28 9 19 414 38236850 38236448 2.390000e-137 499.0
7 TraesCS2D01G088500 chr2D 83.392 283 31 11 3254 3522 38222607 38222327 9.580000e-62 248.0
8 TraesCS2D01G088500 chr2D 87.719 114 12 2 4259 4371 38480088 38479976 1.010000e-26 132.0
9 TraesCS2D01G088500 chr2D 94.828 58 3 0 4401 4458 36259509 36259566 1.710000e-14 91.6
10 TraesCS2D01G088500 chr2D 96.875 32 0 1 3416 3447 38220849 38220819 8.000000e-03 52.8
11 TraesCS2D01G088500 chr2A 91.176 2142 183 4 1061 3201 43299708 43297572 0.000000e+00 2904.0
12 TraesCS2D01G088500 chr2A 80.498 2492 375 62 1065 3521 43282256 43279841 0.000000e+00 1807.0
13 TraesCS2D01G088500 chr2A 89.305 1122 109 5 2097 3216 43286410 43285298 0.000000e+00 1397.0
14 TraesCS2D01G088500 chr2A 86.921 367 43 5 4038 4399 43371054 43370688 1.490000e-109 407.0
15 TraesCS2D01G088500 chr2A 84.083 289 23 4 732 997 43300055 43299767 1.590000e-64 257.0
16 TraesCS2D01G088500 chr2B 82.087 2099 317 36 1096 3172 67081774 67079713 0.000000e+00 1738.0
17 TraesCS2D01G088500 chr2B 88.796 1428 112 22 763 2173 66951201 66949805 0.000000e+00 1707.0
18 TraesCS2D01G088500 chr2B 87.848 1366 160 5 1579 2942 66797729 66796368 0.000000e+00 1598.0
19 TraesCS2D01G088500 chr2B 93.229 1019 69 0 2198 3216 66949812 66948794 0.000000e+00 1500.0
20 TraesCS2D01G088500 chr2B 82.957 1549 224 30 1993 3521 66766579 66765051 0.000000e+00 1362.0
21 TraesCS2D01G088500 chr2B 84.148 757 58 30 1 713 66951938 66951200 0.000000e+00 676.0
22 TraesCS2D01G088500 chr2B 89.423 416 34 5 3992 4401 67066620 67066209 2.380000e-142 516.0
23 TraesCS2D01G088500 chr2B 87.958 382 25 2 1000 1381 66803550 66803190 8.860000e-117 431.0
24 TraesCS2D01G088500 chr2B 85.404 322 31 5 3835 4153 67088520 67088212 2.000000e-83 320.0
25 TraesCS2D01G088500 chr2B 91.031 223 20 0 4179 4401 67088214 67087992 7.250000e-78 302.0
26 TraesCS2D01G088500 chr2B 90.777 206 19 0 1375 1580 66798048 66797843 4.390000e-70 276.0
27 TraesCS2D01G088500 chr2B 87.342 237 21 3 161 391 66804778 66804545 3.420000e-66 263.0
28 TraesCS2D01G088500 chr2B 84.270 267 31 7 151 413 67213248 67212989 2.660000e-62 250.0
29 TraesCS2D01G088500 chr2B 82.609 276 29 11 407 674 66804111 66803847 4.490000e-55 226.0
30 TraesCS2D01G088500 chr2B 83.913 230 25 8 741 964 66803846 66803623 4.520000e-50 209.0
31 TraesCS2D01G088500 chr2B 90.667 150 10 3 3835 3984 67067076 67066931 3.520000e-46 196.0
32 TraesCS2D01G088500 chr2B 93.204 103 7 0 3835 3937 67394424 67394322 7.720000e-33 152.0
33 TraesCS2D01G088500 chr2B 91.463 82 2 2 3176 3252 66948786 66948705 1.700000e-19 108.0
34 TraesCS2D01G088500 chr2B 96.875 32 0 1 3416 3447 67072037 67072007 8.000000e-03 52.8
35 TraesCS2D01G088500 chr7A 70.672 1756 380 81 1072 2776 49991249 49989578 9.510000e-67 265.0
36 TraesCS2D01G088500 chr7D 70.581 1652 380 66 1169 2776 47454081 47455670 1.230000e-65 261.0
37 TraesCS2D01G088500 chr7D 93.103 58 4 0 4401 4458 35820919 35820862 7.950000e-13 86.1
38 TraesCS2D01G088500 chr7D 93.103 58 4 0 4401 4458 543622262 543622319 7.950000e-13 86.1
39 TraesCS2D01G088500 chr7D 93.103 58 4 0 4401 4458 629121077 629121134 7.950000e-13 86.1
40 TraesCS2D01G088500 chr7D 84.416 77 10 2 3706 3781 176163794 176163869 1.720000e-09 75.0
41 TraesCS2D01G088500 chr5A 94.828 58 3 0 4401 4458 579321992 579321935 1.710000e-14 91.6
42 TraesCS2D01G088500 chr4A 94.828 58 3 0 4401 4458 625158835 625158778 1.710000e-14 91.6
43 TraesCS2D01G088500 chr3B 93.548 62 3 1 4397 4458 491374818 491374878 1.710000e-14 91.6
44 TraesCS2D01G088500 chr6D 93.103 58 4 0 4401 4458 401311944 401312001 7.950000e-13 86.1
45 TraesCS2D01G088500 chr4B 93.103 58 4 0 4401 4458 9686182 9686125 7.950000e-13 86.1
46 TraesCS2D01G088500 chr3A 79.688 128 15 10 3714 3835 705295678 705295556 1.030000e-11 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G088500 chr2D 38249392 38253849 4457 True 8233.000000 8233 100.000000 1 4458 1 chr2D.!!$R2 4457
1 TraesCS2D01G088500 chr2D 38440011 38442077 2066 True 1618.000000 1618 81.054000 1079 3158 1 chr2D.!!$R3 2079
2 TraesCS2D01G088500 chr2D 38241636 38242460 824 True 1007.000000 1007 88.551000 3490 4343 1 chr2D.!!$R1 853
3 TraesCS2D01G088500 chr2D 38235266 38236850 1584 True 764.000000 1029 89.549000 19 1802 2 chr2D.!!$R7 1783
4 TraesCS2D01G088500 chr2D 38216304 38222607 6303 True 709.266667 1827 87.169667 1186 3522 3 chr2D.!!$R6 2336
5 TraesCS2D01G088500 chr2D 38548482 38549047 565 True 691.000000 691 88.831000 3835 4401 1 chr2D.!!$R5 566
6 TraesCS2D01G088500 chr2A 43279841 43286410 6569 True 1602.000000 1807 84.901500 1065 3521 2 chr2A.!!$R2 2456
7 TraesCS2D01G088500 chr2A 43297572 43300055 2483 True 1580.500000 2904 87.629500 732 3201 2 chr2A.!!$R3 2469
8 TraesCS2D01G088500 chr2B 67079713 67081774 2061 True 1738.000000 1738 82.087000 1096 3172 1 chr2B.!!$R3 2076
9 TraesCS2D01G088500 chr2B 66765051 66766579 1528 True 1362.000000 1362 82.957000 1993 3521 1 chr2B.!!$R1 1528
10 TraesCS2D01G088500 chr2B 66948705 66951938 3233 True 997.750000 1707 89.409000 1 3252 4 chr2B.!!$R8 3251
11 TraesCS2D01G088500 chr2B 66796368 66798048 1680 True 937.000000 1598 89.312500 1375 2942 2 chr2B.!!$R6 1567
12 TraesCS2D01G088500 chr2B 67066209 67067076 867 True 356.000000 516 90.045000 3835 4401 2 chr2B.!!$R9 566
13 TraesCS2D01G088500 chr2B 67087992 67088520 528 True 311.000000 320 88.217500 3835 4401 2 chr2B.!!$R10 566
14 TraesCS2D01G088500 chr2B 66803190 66804778 1588 True 282.250000 431 85.455500 161 1381 4 chr2B.!!$R7 1220
15 TraesCS2D01G088500 chr7A 49989578 49991249 1671 True 265.000000 265 70.672000 1072 2776 1 chr7A.!!$R1 1704
16 TraesCS2D01G088500 chr7D 47454081 47455670 1589 False 261.000000 261 70.581000 1169 2776 1 chr7D.!!$F1 1607

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
134 144 0.247460 CACTGCATCTTCCTCCGACA 59.753 55.0 0.0 0.0 0.0 4.35 F
1594 4851 0.876777 CCACAACAAGTACGTCGGCA 60.877 55.0 0.0 0.0 0.0 5.69 F
2653 5952 0.110678 TGCCGTTGAAACCACCCATA 59.889 50.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 5376 0.768221 ACCTCCCAGTCCTCTTGCAA 60.768 55.0 0.00 0.00 0.00 4.08 R
3260 6617 0.107508 AGTTCCGACATGCAGGATGG 60.108 55.0 4.84 6.31 36.23 3.51 R
3794 7157 0.031917 TTGATAGCCTGGTACCCGGA 60.032 55.0 25.39 6.38 29.82 5.14 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 9.729281 AATGCTTCATTTGGAGTCAATAAAATT 57.271 25.926 0.00 0.00 28.76 1.82
134 144 0.247460 CACTGCATCTTCCTCCGACA 59.753 55.000 0.00 0.00 0.00 4.35
135 145 1.134580 CACTGCATCTTCCTCCGACAT 60.135 52.381 0.00 0.00 0.00 3.06
149 159 5.597182 TCCTCCGACATAGTTGCTATTAGTT 59.403 40.000 0.00 0.00 0.00 2.24
254 270 3.488310 GCAAGCTGTCAGAAAACACAATG 59.512 43.478 3.32 0.00 0.00 2.82
268 284 6.833342 AAACACAATGCTGAAAAGATTCAC 57.167 33.333 0.00 0.00 40.59 3.18
272 288 2.975410 TGCTGAAAAGATTCACGCAG 57.025 45.000 9.84 0.00 40.98 5.18
299 315 6.302269 AGTCAGTTGAAAAGATCCAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
332 349 4.820716 GCTCATATTATCCATGGAGATGCC 59.179 45.833 21.33 10.63 37.10 4.40
492 938 9.226345 GAAGTGAAGTGAGTTTTTCAAACTATG 57.774 33.333 1.85 0.00 37.61 2.23
497 943 9.665264 GAAGTGAGTTTTTCAAACTATGTTAGG 57.335 33.333 1.85 0.00 37.61 2.69
557 1027 1.263484 CTCATGCCTCATTGCTAAGCG 59.737 52.381 0.00 0.00 0.00 4.68
692 1162 2.564062 AGAGGGTTGATGGCATTTGTTG 59.436 45.455 0.00 0.00 0.00 3.33
872 1346 1.575576 CCGTCGTCTCACGTCTCCTT 61.576 60.000 0.00 0.00 43.14 3.36
1146 4243 3.482783 GCCGTTCGCTGCTGTCTC 61.483 66.667 0.00 0.00 0.00 3.36
1147 4244 3.175240 CCGTTCGCTGCTGTCTCG 61.175 66.667 0.00 0.00 0.00 4.04
1148 4245 2.429236 CGTTCGCTGCTGTCTCGT 60.429 61.111 0.00 0.00 0.00 4.18
1149 4246 2.710971 CGTTCGCTGCTGTCTCGTG 61.711 63.158 0.00 0.00 0.00 4.35
1150 4247 2.049156 TTCGCTGCTGTCTCGTGG 60.049 61.111 0.00 0.00 0.00 4.94
1151 4248 4.724602 TCGCTGCTGTCTCGTGGC 62.725 66.667 0.00 0.00 0.00 5.01
1286 4416 2.517402 GACCAACGGTGCCACCAA 60.517 61.111 15.45 0.00 38.47 3.67
1324 4454 4.954118 TCCACCCGTCCCTGCTGT 62.954 66.667 0.00 0.00 0.00 4.40
1421 4551 2.813908 CCAGCACGCCGACCTTAC 60.814 66.667 0.00 0.00 0.00 2.34
1425 4555 2.048877 CACGCCGACCTTACCGTT 60.049 61.111 0.00 0.00 0.00 4.44
1570 4712 1.429148 CTACAATGCCGAGTTCCGCC 61.429 60.000 0.00 0.00 36.84 6.13
1594 4851 0.876777 CCACAACAAGTACGTCGGCA 60.877 55.000 0.00 0.00 0.00 5.69
1680 4940 3.181468 GGCGGCTACTAAACCTATCTGTT 60.181 47.826 0.00 0.00 0.00 3.16
1743 5003 5.005740 GGCATGGCAAAGATGATCAGTATA 58.994 41.667 15.47 0.00 0.00 1.47
1769 5029 3.410628 TCCGCTGGGCATGGTCAT 61.411 61.111 0.00 0.00 0.00 3.06
1974 5243 1.476833 GCCTGGACCAAGAACAACTCA 60.477 52.381 0.00 0.00 0.00 3.41
2081 5362 1.132453 CATCTCTACAAGACGGCGTCA 59.868 52.381 37.71 19.04 36.65 4.35
2082 5363 1.241165 TCTCTACAAGACGGCGTCAA 58.759 50.000 37.71 20.48 34.60 3.18
2095 5376 0.517316 GCGTCAAAATTGCTCCGAGT 59.483 50.000 0.00 0.00 0.00 4.18
2172 5453 0.400213 TTCATGCGACAGAGGGGTTT 59.600 50.000 0.00 0.00 0.00 3.27
2447 5740 2.158534 ACCTACACACAAGAAATGGCCA 60.159 45.455 8.56 8.56 0.00 5.36
2536 5835 1.134280 AGGAATGGGAGCAAGTCATCG 60.134 52.381 0.00 0.00 0.00 3.84
2568 5867 7.041780 CGAGATATAAAGGCAAGTAATGTGCTT 60.042 37.037 0.00 0.00 41.88 3.91
2639 5938 0.319083 TATGACCACGAAACTGCCGT 59.681 50.000 0.00 0.00 41.36 5.68
2653 5952 0.110678 TGCCGTTGAAACCACCCATA 59.889 50.000 0.00 0.00 0.00 2.74
2697 5996 1.837051 ACCAGAACTCTCCCGTGCA 60.837 57.895 0.00 0.00 0.00 4.57
2754 6055 2.288825 TGGCGTGTTTCTTCTAGAGGTG 60.289 50.000 1.31 0.00 0.00 4.00
2863 6164 0.740868 AATGCTCGACACGGTGGATG 60.741 55.000 13.48 1.72 0.00 3.51
2872 6173 2.261361 CGGTGGATGCACGACTCA 59.739 61.111 11.52 0.00 0.00 3.41
2943 6244 1.677637 TATGCACGTACCCATCGCCA 61.678 55.000 0.00 0.00 0.00 5.69
2967 6268 2.398554 GCGGCCTCTCATGCGAAAA 61.399 57.895 0.00 0.00 0.00 2.29
2997 6298 5.430886 CAGTACCTTGACCATGATCAATCA 58.569 41.667 2.08 1.23 37.93 2.57
3012 6313 6.226052 TGATCAATCACCTCCTGATTTATCG 58.774 40.000 0.00 0.00 45.89 2.92
3031 6332 0.320508 GCCGGCCTACATAAGCTACC 60.321 60.000 18.11 0.00 0.00 3.18
3067 6368 6.348704 CCAAATGCAAAATGAAGGGTTTGATC 60.349 38.462 0.00 0.00 36.96 2.92
3074 6375 2.862541 TGAAGGGTTTGATCCACACAG 58.137 47.619 0.00 0.00 0.00 3.66
3078 6379 2.308570 AGGGTTTGATCCACACAGCATA 59.691 45.455 0.00 0.00 0.00 3.14
3089 6390 2.349580 CACACAGCATACCATGTTCTCG 59.650 50.000 0.00 0.00 0.00 4.04
3091 6392 3.261580 CACAGCATACCATGTTCTCGAA 58.738 45.455 0.00 0.00 0.00 3.71
3213 6569 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3215 6571 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3258 6615 8.420374 TGTATTAAGAAGTTATGCTACACTGC 57.580 34.615 0.00 0.00 0.00 4.40
3260 6617 7.778470 ATTAAGAAGTTATGCTACACTGCTC 57.222 36.000 0.00 0.00 27.55 4.26
3262 6619 3.515502 AGAAGTTATGCTACACTGCTCCA 59.484 43.478 0.00 0.00 0.00 3.86
3295 6652 2.943993 GAACTGTCCGTTCTCTGGTAC 58.056 52.381 0.25 0.00 46.74 3.34
3298 6655 3.693807 ACTGTCCGTTCTCTGGTACATA 58.306 45.455 0.00 0.00 38.20 2.29
3300 6657 4.158025 ACTGTCCGTTCTCTGGTACATAAG 59.842 45.833 0.00 0.00 38.20 1.73
3307 6664 5.548406 GTTCTCTGGTACATAAGTGTTGGT 58.452 41.667 0.00 0.00 39.77 3.67
3309 6666 6.182507 TCTCTGGTACATAAGTGTTGGTTT 57.817 37.500 0.00 0.00 39.77 3.27
3314 6671 7.604927 TCTGGTACATAAGTGTTGGTTTATCAC 59.395 37.037 0.00 0.00 39.77 3.06
3357 6714 7.761249 AGTGGTTAAGAAAATTTCATGCATAGC 59.239 33.333 8.55 0.00 0.00 2.97
3373 6730 4.261801 GCATAGCTTTGAAGGTTGGAGTA 58.738 43.478 8.49 0.00 37.92 2.59
3383 6740 7.549147 TTGAAGGTTGGAGTATACAAGTACT 57.451 36.000 5.50 0.00 37.61 2.73
3384 6741 7.166691 TGAAGGTTGGAGTATACAAGTACTC 57.833 40.000 5.50 5.69 46.29 2.59
3385 6742 6.952358 TGAAGGTTGGAGTATACAAGTACTCT 59.048 38.462 5.50 0.00 46.26 3.24
3386 6743 6.777213 AGGTTGGAGTATACAAGTACTCTG 57.223 41.667 5.50 0.00 46.26 3.35
3387 6744 6.491383 AGGTTGGAGTATACAAGTACTCTGA 58.509 40.000 5.50 1.63 46.26 3.27
3388 6745 7.126733 AGGTTGGAGTATACAAGTACTCTGAT 58.873 38.462 5.50 0.00 46.26 2.90
3389 6746 7.068839 AGGTTGGAGTATACAAGTACTCTGATG 59.931 40.741 5.50 0.00 46.26 3.07
3390 6747 7.068348 GGTTGGAGTATACAAGTACTCTGATGA 59.932 40.741 5.50 0.00 46.26 2.92
3391 6748 7.809546 TGGAGTATACAAGTACTCTGATGAG 57.190 40.000 5.50 0.00 46.26 2.90
3411 6768 1.136029 GTCGTCGTCTCGTTGATCAGT 60.136 52.381 0.00 0.00 0.00 3.41
3414 6771 1.469308 GTCGTCTCGTTGATCAGTCCT 59.531 52.381 0.00 0.00 0.00 3.85
3446 6803 3.913548 TTGTGTCCACCAAATGAATCG 57.086 42.857 0.00 0.00 0.00 3.34
3447 6804 2.857483 TGTGTCCACCAAATGAATCGT 58.143 42.857 0.00 0.00 0.00 3.73
3448 6805 3.218453 TGTGTCCACCAAATGAATCGTT 58.782 40.909 0.00 0.00 0.00 3.85
3449 6806 3.004210 TGTGTCCACCAAATGAATCGTTG 59.996 43.478 0.00 0.00 0.00 4.10
3450 6807 3.004315 GTGTCCACCAAATGAATCGTTGT 59.996 43.478 0.00 0.00 0.00 3.32
3451 6808 3.634448 TGTCCACCAAATGAATCGTTGTT 59.366 39.130 0.00 0.00 0.00 2.83
3459 6821 9.995957 CACCAAATGAATCGTTGTTACATATTA 57.004 29.630 0.00 0.00 0.00 0.98
3460 6822 9.997482 ACCAAATGAATCGTTGTTACATATTAC 57.003 29.630 0.00 0.00 0.00 1.89
3463 6825 9.910511 AAATGAATCGTTGTTACATATTACGTC 57.089 29.630 7.10 0.66 34.15 4.34
3464 6826 7.453980 TGAATCGTTGTTACATATTACGTCC 57.546 36.000 7.10 0.51 34.15 4.79
3466 6828 7.433131 TGAATCGTTGTTACATATTACGTCCTC 59.567 37.037 7.10 4.17 34.15 3.71
3475 6837 6.222038 ACATATTACGTCCTCATGAACAGT 57.778 37.500 0.00 0.00 0.00 3.55
3476 6838 6.042777 ACATATTACGTCCTCATGAACAGTG 58.957 40.000 0.00 0.00 0.00 3.66
3487 6849 3.503363 TCATGAACAGTGTGATTGAAGGC 59.497 43.478 0.00 0.00 0.00 4.35
3499 6861 1.737838 TTGAAGGCCAAGAGCATACG 58.262 50.000 5.01 0.00 46.50 3.06
3512 6874 4.122776 AGAGCATACGTTCACATGATTCC 58.877 43.478 0.00 0.00 0.00 3.01
3534 6896 0.249699 TGGTTGTGCTCGTGATCGTT 60.250 50.000 0.00 0.00 38.33 3.85
3543 6905 1.395954 CTCGTGATCGTTAGTCCGTGA 59.604 52.381 0.00 0.00 38.33 4.35
3548 6910 2.418976 TGATCGTTAGTCCGTGACTGAG 59.581 50.000 14.50 7.47 43.30 3.35
3551 6913 2.738846 TCGTTAGTCCGTGACTGAGTAC 59.261 50.000 14.50 7.91 43.30 2.73
3573 6935 3.897122 GACACTGGGTTGGGGCCA 61.897 66.667 4.39 0.00 0.00 5.36
3574 6936 4.218686 ACACTGGGTTGGGGCCAC 62.219 66.667 4.39 0.00 0.00 5.01
3588 6951 1.026718 GGCCACCTGATCTTTGTCCG 61.027 60.000 0.00 0.00 0.00 4.79
3605 6968 2.673074 CGGTGGCATGTTACTACCG 58.327 57.895 11.21 11.21 46.66 4.02
3606 6969 3.074594 GGTGGCATGTTACTACCGG 57.925 57.895 0.00 0.00 0.00 5.28
3610 6973 1.481772 TGGCATGTTACTACCGGGTAC 59.518 52.381 6.32 0.00 0.00 3.34
3632 6995 0.669318 TTGTGTTCGATCACCGGCTC 60.669 55.000 20.87 0.00 37.51 4.70
3657 7020 2.514824 GATCCCCTTGCAGACGGC 60.515 66.667 0.00 0.00 45.13 5.68
3669 7032 0.036010 CAGACGGCAAGATCCCTGTT 60.036 55.000 0.00 0.00 0.00 3.16
3680 7043 3.235200 AGATCCCTGTTAATCTCCTCCG 58.765 50.000 0.00 0.00 0.00 4.63
3700 7063 0.680280 GGTACCGCTGAGGAGAGTGA 60.680 60.000 3.87 0.00 45.00 3.41
3707 7070 3.070018 CGCTGAGGAGAGTGAAATGTTT 58.930 45.455 0.00 0.00 0.00 2.83
3708 7071 4.245660 CGCTGAGGAGAGTGAAATGTTTA 58.754 43.478 0.00 0.00 0.00 2.01
3711 7074 6.128172 CGCTGAGGAGAGTGAAATGTTTATTT 60.128 38.462 0.00 0.00 39.16 1.40
3712 7075 7.064609 CGCTGAGGAGAGTGAAATGTTTATTTA 59.935 37.037 0.00 0.00 36.66 1.40
3755 7118 9.581289 TTGTAAAGAGATAAAACCAATGGAAGA 57.419 29.630 6.16 0.00 0.00 2.87
3756 7119 9.231297 TGTAAAGAGATAAAACCAATGGAAGAG 57.769 33.333 6.16 0.00 0.00 2.85
3758 7121 6.394345 AGAGATAAAACCAATGGAAGAGGT 57.606 37.500 6.16 0.00 37.20 3.85
3760 7123 5.264395 AGATAAAACCAATGGAAGAGGTGG 58.736 41.667 6.16 0.00 35.42 4.61
3762 7125 2.292828 AACCAATGGAAGAGGTGGTG 57.707 50.000 6.16 0.00 43.62 4.17
3763 7126 0.405585 ACCAATGGAAGAGGTGGTGG 59.594 55.000 6.16 0.00 42.79 4.61
3764 7127 0.323725 CCAATGGAAGAGGTGGTGGG 60.324 60.000 0.00 0.00 0.00 4.61
3765 7128 0.698238 CAATGGAAGAGGTGGTGGGA 59.302 55.000 0.00 0.00 0.00 4.37
3766 7129 0.995024 AATGGAAGAGGTGGTGGGAG 59.005 55.000 0.00 0.00 0.00 4.30
3767 7130 0.119155 ATGGAAGAGGTGGTGGGAGA 59.881 55.000 0.00 0.00 0.00 3.71
3768 7131 0.119155 TGGAAGAGGTGGTGGGAGAT 59.881 55.000 0.00 0.00 0.00 2.75
3769 7132 0.543749 GGAAGAGGTGGTGGGAGATG 59.456 60.000 0.00 0.00 0.00 2.90
3770 7133 0.543749 GAAGAGGTGGTGGGAGATGG 59.456 60.000 0.00 0.00 0.00 3.51
3771 7134 0.119155 AAGAGGTGGTGGGAGATGGA 59.881 55.000 0.00 0.00 0.00 3.41
3772 7135 0.344790 AGAGGTGGTGGGAGATGGAT 59.655 55.000 0.00 0.00 0.00 3.41
3773 7136 0.471617 GAGGTGGTGGGAGATGGATG 59.528 60.000 0.00 0.00 0.00 3.51
3819 7182 2.706190 GGTACCAGGCTATCAACTCCAT 59.294 50.000 7.15 0.00 0.00 3.41
3820 7183 3.244249 GGTACCAGGCTATCAACTCCATC 60.244 52.174 7.15 0.00 0.00 3.51
3821 7184 2.769209 ACCAGGCTATCAACTCCATCT 58.231 47.619 0.00 0.00 0.00 2.90
3822 7185 3.118531 ACCAGGCTATCAACTCCATCTT 58.881 45.455 0.00 0.00 0.00 2.40
3823 7186 3.525199 ACCAGGCTATCAACTCCATCTTT 59.475 43.478 0.00 0.00 0.00 2.52
3824 7187 4.018050 ACCAGGCTATCAACTCCATCTTTT 60.018 41.667 0.00 0.00 0.00 2.27
3825 7188 4.337555 CCAGGCTATCAACTCCATCTTTTG 59.662 45.833 0.00 0.00 0.00 2.44
3919 7285 6.595716 GCATCACCTGAACTTAGAATACTTGT 59.404 38.462 0.00 0.00 0.00 3.16
3942 7308 4.737054 ACCAAAATCAGCAACGATGATTC 58.263 39.130 7.82 0.00 45.95 2.52
3963 7329 4.307259 TCCCCTATAAAGAATCACCAGCT 58.693 43.478 0.00 0.00 0.00 4.24
3964 7330 5.473273 TCCCCTATAAAGAATCACCAGCTA 58.527 41.667 0.00 0.00 0.00 3.32
3965 7331 6.091555 TCCCCTATAAAGAATCACCAGCTAT 58.908 40.000 0.00 0.00 0.00 2.97
3966 7332 7.253421 TCCCCTATAAAGAATCACCAGCTATA 58.747 38.462 0.00 0.00 0.00 1.31
3967 7333 7.906736 TCCCCTATAAAGAATCACCAGCTATAT 59.093 37.037 0.00 0.00 0.00 0.86
3987 7353 2.409948 ATAAACCCTGCAGCTGAGAC 57.590 50.000 20.43 0.00 0.00 3.36
4036 7707 4.220382 CCAGGTGAAAATATTCAGGCACAA 59.780 41.667 0.00 0.00 45.88 3.33
4042 7713 6.369615 GTGAAAATATTCAGGCACAAGCAAAT 59.630 34.615 0.00 0.00 45.88 2.32
4059 7730 5.828747 AGCAAATGATGTTCATGCTGATAC 58.171 37.500 5.13 0.00 40.16 2.24
4100 7771 6.261435 TCTAGAAAAGACCCTGTCCAGAATA 58.739 40.000 0.00 0.00 32.18 1.75
4268 7943 5.827367 CCGATGGCGTTCGTAAGATAACAG 61.827 50.000 8.53 0.00 39.91 3.16
4294 7969 1.160137 GTTCAGCTGCAAACTCCGAT 58.840 50.000 9.47 0.00 0.00 4.18
4295 7970 1.129437 GTTCAGCTGCAAACTCCGATC 59.871 52.381 9.47 0.00 0.00 3.69
4296 7971 0.737367 TCAGCTGCAAACTCCGATCG 60.737 55.000 9.47 8.51 0.00 3.69
4315 7990 5.804979 CGATCGGAGCCAAACAAATTAATTT 59.195 36.000 7.38 7.64 0.00 1.82
4353 8028 1.258458 TCTTAAAACACGACAACGGCG 59.742 47.619 4.80 4.80 44.46 6.46
4371 8047 1.139989 CGGCGATGATAAGCGTTCAT 58.860 50.000 0.00 0.00 36.54 2.57
4373 8049 2.135139 GGCGATGATAAGCGTTCATGA 58.865 47.619 0.00 0.00 34.03 3.07
4375 8051 3.926527 GGCGATGATAAGCGTTCATGATA 59.073 43.478 0.00 0.00 34.03 2.15
4401 8077 4.887655 GCCAAAACCTGTAATAGTGCCTAT 59.112 41.667 0.00 0.00 0.00 2.57
4402 8078 6.059484 GCCAAAACCTGTAATAGTGCCTATA 58.941 40.000 0.00 0.00 0.00 1.31
4403 8079 6.204882 GCCAAAACCTGTAATAGTGCCTATAG 59.795 42.308 0.00 0.00 0.00 1.31
4404 8080 7.280356 CCAAAACCTGTAATAGTGCCTATAGT 58.720 38.462 0.00 0.00 0.00 2.12
4405 8081 7.773690 CCAAAACCTGTAATAGTGCCTATAGTT 59.226 37.037 0.00 0.00 0.00 2.24
4406 8082 9.174166 CAAAACCTGTAATAGTGCCTATAGTTT 57.826 33.333 0.00 0.00 0.00 2.66
4407 8083 9.749340 AAAACCTGTAATAGTGCCTATAGTTTT 57.251 29.630 0.00 0.00 0.00 2.43
4416 8092 8.773404 ATAGTGCCTATAGTTTTAAATAGCCG 57.227 34.615 0.00 0.00 0.00 5.52
4417 8093 5.995897 AGTGCCTATAGTTTTAAATAGCCGG 59.004 40.000 0.00 0.00 0.00 6.13
4418 8094 4.758165 TGCCTATAGTTTTAAATAGCCGGC 59.242 41.667 21.89 21.89 0.00 6.13
4419 8095 5.001874 GCCTATAGTTTTAAATAGCCGGCT 58.998 41.667 34.85 34.85 0.00 5.52
4420 8096 6.168389 GCCTATAGTTTTAAATAGCCGGCTA 58.832 40.000 36.88 36.88 0.00 3.93
4421 8097 6.822170 GCCTATAGTTTTAAATAGCCGGCTAT 59.178 38.462 37.79 37.79 40.63 2.97
4422 8098 7.983484 GCCTATAGTTTTAAATAGCCGGCTATA 59.017 37.037 41.53 28.18 38.20 1.31
4423 8099 9.530633 CCTATAGTTTTAAATAGCCGGCTATAG 57.469 37.037 41.53 30.14 38.20 1.31
4424 8100 7.845066 ATAGTTTTAAATAGCCGGCTATAGC 57.155 36.000 41.53 29.09 38.20 2.97
4425 8101 5.866207 AGTTTTAAATAGCCGGCTATAGCT 58.134 37.500 41.53 30.55 43.20 3.32
4426 8102 5.932883 AGTTTTAAATAGCCGGCTATAGCTC 59.067 40.000 41.53 28.58 40.56 4.09
4427 8103 4.467198 TTAAATAGCCGGCTATAGCTCC 57.533 45.455 41.53 12.16 40.56 4.70
4428 8104 0.818296 AATAGCCGGCTATAGCTCCG 59.182 55.000 41.53 18.50 44.89 4.63
4429 8105 0.323542 ATAGCCGGCTATAGCTCCGT 60.324 55.000 41.03 20.49 43.87 4.69
4430 8106 0.538977 TAGCCGGCTATAGCTCCGTT 60.539 55.000 32.24 6.88 43.87 4.44
4431 8107 0.538977 AGCCGGCTATAGCTCCGTTA 60.539 55.000 31.86 0.00 43.87 3.18
4432 8108 0.531200 GCCGGCTATAGCTCCGTTAT 59.469 55.000 22.15 0.00 43.87 1.89
4433 8109 1.067071 GCCGGCTATAGCTCCGTTATT 60.067 52.381 22.15 0.00 43.87 1.40
4434 8110 2.607187 CCGGCTATAGCTCCGTTATTG 58.393 52.381 23.53 3.89 43.87 1.90
4435 8111 1.993370 CGGCTATAGCTCCGTTATTGC 59.007 52.381 23.53 2.73 40.72 3.56
4436 8112 2.347731 GGCTATAGCTCCGTTATTGCC 58.652 52.381 23.53 3.62 39.28 4.52
4437 8113 2.028020 GGCTATAGCTCCGTTATTGCCT 60.028 50.000 23.53 0.00 41.39 4.75
4438 8114 3.557264 GGCTATAGCTCCGTTATTGCCTT 60.557 47.826 23.53 0.00 41.39 4.35
4439 8115 4.065789 GCTATAGCTCCGTTATTGCCTTT 58.934 43.478 17.75 0.00 38.21 3.11
4440 8116 4.515567 GCTATAGCTCCGTTATTGCCTTTT 59.484 41.667 17.75 0.00 38.21 2.27
4441 8117 5.334182 GCTATAGCTCCGTTATTGCCTTTTC 60.334 44.000 17.75 0.00 38.21 2.29
4442 8118 2.790433 AGCTCCGTTATTGCCTTTTCA 58.210 42.857 0.00 0.00 0.00 2.69
4443 8119 2.749621 AGCTCCGTTATTGCCTTTTCAG 59.250 45.455 0.00 0.00 0.00 3.02
4444 8120 2.488153 GCTCCGTTATTGCCTTTTCAGT 59.512 45.455 0.00 0.00 0.00 3.41
4445 8121 3.687698 GCTCCGTTATTGCCTTTTCAGTA 59.312 43.478 0.00 0.00 0.00 2.74
4446 8122 4.155280 GCTCCGTTATTGCCTTTTCAGTAA 59.845 41.667 0.00 0.00 0.00 2.24
4447 8123 5.673818 GCTCCGTTATTGCCTTTTCAGTAAG 60.674 44.000 0.00 0.00 0.00 2.34
4448 8124 4.698304 TCCGTTATTGCCTTTTCAGTAAGG 59.302 41.667 0.00 0.00 46.14 2.69
4449 8125 4.457949 CCGTTATTGCCTTTTCAGTAAGGT 59.542 41.667 0.00 0.00 45.34 3.50
4450 8126 5.390613 CGTTATTGCCTTTTCAGTAAGGTG 58.609 41.667 0.00 0.00 45.34 4.00
4451 8127 3.942130 ATTGCCTTTTCAGTAAGGTGC 57.058 42.857 0.00 0.00 45.34 5.01
4452 8128 1.616159 TGCCTTTTCAGTAAGGTGCC 58.384 50.000 0.00 0.00 45.34 5.01
4453 8129 0.521735 GCCTTTTCAGTAAGGTGCCG 59.478 55.000 0.00 0.00 45.34 5.69
4454 8130 0.521735 CCTTTTCAGTAAGGTGCCGC 59.478 55.000 0.00 0.00 39.89 6.53
4455 8131 1.523758 CTTTTCAGTAAGGTGCCGCT 58.476 50.000 0.00 0.00 0.00 5.52
4456 8132 2.614481 CCTTTTCAGTAAGGTGCCGCTA 60.614 50.000 0.00 0.00 39.89 4.26
4457 8133 2.843401 TTTCAGTAAGGTGCCGCTAA 57.157 45.000 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 75 6.942532 ATTGATAGTACAATCCAACGCAAT 57.057 33.333 0.00 0.00 35.92 3.56
254 270 1.537202 ACCTGCGTGAATCTTTTCAGC 59.463 47.619 0.00 0.00 42.41 4.26
268 284 3.390135 TCTTTTCAACTGACTACCTGCG 58.610 45.455 0.00 0.00 0.00 5.18
272 288 5.639931 GTCTGGATCTTTTCAACTGACTACC 59.360 44.000 0.00 0.00 0.00 3.18
299 315 7.338449 CCATGGATAATATGAGCATGAACATCA 59.662 37.037 5.56 0.00 0.00 3.07
392 413 9.852091 GATTTTGTCTCTTCATGCTCTTTATTT 57.148 29.630 0.00 0.00 0.00 1.40
421 861 4.564769 GTCTGAATGTTTCTCGATGACTCC 59.435 45.833 0.00 0.00 0.00 3.85
487 933 5.761165 ACGTTTTTGCAACCTAACATAGT 57.239 34.783 0.00 0.00 0.00 2.12
492 938 8.684655 GTTAGAATTACGTTTTTGCAACCTAAC 58.315 33.333 0.00 3.43 0.00 2.34
497 943 7.901874 TCTGTTAGAATTACGTTTTTGCAAC 57.098 32.000 0.00 0.00 0.00 4.17
557 1027 6.319911 AGGTCTTCAGGAGCAAAATATTTAGC 59.680 38.462 0.01 0.00 44.16 3.09
692 1162 2.601367 TGCAGCCTGCTTTTCCCC 60.601 61.111 18.96 0.00 45.31 4.81
738 1208 3.868661 TGTAACGCGTGCATGATAAATCT 59.131 39.130 14.98 0.00 0.00 2.40
872 1346 2.832129 ACTGTCTAGGCGATCCTTTTCA 59.168 45.455 0.00 0.00 40.66 2.69
1132 4229 2.375766 CCACGAGACAGCAGCGAAC 61.376 63.158 0.00 0.00 0.00 3.95
1133 4230 2.049156 CCACGAGACAGCAGCGAA 60.049 61.111 0.00 0.00 0.00 4.70
1134 4231 4.724602 GCCACGAGACAGCAGCGA 62.725 66.667 0.00 0.00 0.00 4.93
1174 4298 2.009108 CGAACTGCCGACCATCATG 58.991 57.895 0.00 0.00 0.00 3.07
1324 4454 4.367023 CGACCCGGAGCCGAACAA 62.367 66.667 11.05 0.00 42.83 2.83
1570 4712 2.154963 CGACGTACTTGTTGTGGATGTG 59.845 50.000 0.00 0.00 0.00 3.21
1594 4851 1.676529 CACCAGACTATCACCGTCGAT 59.323 52.381 0.00 0.00 36.53 3.59
1702 4962 1.601419 CCGTCGTAGTCCACCCACAT 61.601 60.000 0.00 0.00 0.00 3.21
1769 5029 2.681064 GCATGGGCTTCTTGGGCA 60.681 61.111 0.00 0.00 36.96 5.36
1830 5096 1.441515 CGACGAGAAGCCGACGAAA 60.442 57.895 0.00 0.00 46.78 3.46
1832 5098 3.796443 CCGACGAGAAGCCGACGA 61.796 66.667 9.33 0.00 46.78 4.20
1974 5243 3.055167 TGGACATGAACGATGAGTTGGAT 60.055 43.478 0.00 0.00 44.35 3.41
2095 5376 0.768221 ACCTCCCAGTCCTCTTGCAA 60.768 55.000 0.00 0.00 0.00 4.08
2172 5453 2.303022 CCCAAGCAGGTTCTTCTCACTA 59.697 50.000 0.00 0.00 34.66 2.74
2270 5563 1.632589 AACCCCTTGCCTTGAATCAC 58.367 50.000 0.00 0.00 0.00 3.06
2334 5627 6.545666 AGCCCAATAATTGTGTGATATTTCGA 59.454 34.615 0.00 0.00 0.00 3.71
2369 5662 3.532102 ACCAGGAGAAGTTCACCCTTAT 58.468 45.455 14.94 4.12 0.00 1.73
2447 5740 3.195825 CCTCTCGGACCAACATAGAGTTT 59.804 47.826 0.00 0.00 38.74 2.66
2536 5835 3.746045 TGCCTTTATATCTCGGTGGAC 57.254 47.619 0.00 0.00 0.00 4.02
2568 5867 4.023279 CGTCCATTCATCTTGTTGTCCAAA 60.023 41.667 0.00 0.00 31.20 3.28
2576 5875 2.436417 CCAACCGTCCATTCATCTTGT 58.564 47.619 0.00 0.00 0.00 3.16
2639 5938 2.917713 AGCCATATGGGTGGTTTCAA 57.082 45.000 25.40 0.00 45.50 2.69
2745 6046 2.092323 CGTCCACATGTCACCTCTAGA 58.908 52.381 0.00 0.00 0.00 2.43
2754 6055 3.127533 GGCCTGCGTCCACATGTC 61.128 66.667 0.00 0.00 0.00 3.06
2808 6109 1.668294 CTCAAGCACCCACTCGACT 59.332 57.895 0.00 0.00 0.00 4.18
2863 6164 0.250513 AATTCCCCTCTGAGTCGTGC 59.749 55.000 3.66 0.00 0.00 5.34
2872 6173 1.279271 CTCCGTGTTGAATTCCCCTCT 59.721 52.381 2.27 0.00 0.00 3.69
2943 6244 4.760047 ATGAGAGGCCGCGCGTTT 62.760 61.111 29.95 13.62 0.00 3.60
2956 6257 2.161012 ACTGCATGACTTTTCGCATGAG 59.839 45.455 0.00 0.00 43.43 2.90
2967 6268 1.977854 TGGTCAAGGTACTGCATGACT 59.022 47.619 13.85 0.00 40.86 3.41
2997 6298 0.393077 CCGGCGATAAATCAGGAGGT 59.607 55.000 9.30 0.00 0.00 3.85
3012 6313 0.320508 GGTAGCTTATGTAGGCCGGC 60.321 60.000 21.18 21.18 0.00 6.13
3031 6332 1.116308 TGCATTTGGGCCATCATGAG 58.884 50.000 23.84 7.30 0.00 2.90
3067 6368 2.679837 GAGAACATGGTATGCTGTGTGG 59.320 50.000 0.00 0.00 0.00 4.17
3074 6375 1.593006 CGGTTCGAGAACATGGTATGC 59.407 52.381 16.56 0.00 42.85 3.14
3078 6379 0.250124 TTGCGGTTCGAGAACATGGT 60.250 50.000 16.56 0.00 42.85 3.55
3089 6390 1.132640 GCGACACTCATTGCGGTTC 59.867 57.895 0.00 0.00 0.00 3.62
3091 6392 2.742372 GGCGACACTCATTGCGGT 60.742 61.111 0.00 0.00 0.00 5.68
3213 6569 4.398319 ACAACTCCTTACCACCAAATGAG 58.602 43.478 0.00 0.00 0.00 2.90
3215 6571 6.834168 AATACAACTCCTTACCACCAAATG 57.166 37.500 0.00 0.00 0.00 2.32
3252 6609 0.393944 CATGCAGGATGGAGCAGTGT 60.394 55.000 0.00 0.00 42.42 3.55
3255 6612 1.158484 CGACATGCAGGATGGAGCAG 61.158 60.000 4.84 0.00 42.42 4.24
3258 6615 0.178767 TTCCGACATGCAGGATGGAG 59.821 55.000 4.84 0.00 42.42 3.86
3260 6617 0.107508 AGTTCCGACATGCAGGATGG 60.108 55.000 4.84 6.31 36.23 3.51
3262 6619 0.615331 ACAGTTCCGACATGCAGGAT 59.385 50.000 4.84 0.00 36.28 3.24
3284 6641 5.548406 ACCAACACTTATGTACCAGAGAAC 58.452 41.667 0.00 0.00 38.45 3.01
3287 6644 7.822334 TGATAAACCAACACTTATGTACCAGAG 59.178 37.037 0.00 0.00 38.45 3.35
3291 6648 7.916914 AGTGATAAACCAACACTTATGTACC 57.083 36.000 0.00 0.00 41.21 3.34
3328 6685 7.495901 TGCATGAAATTTTCTTAACCACTTGA 58.504 30.769 10.33 0.00 0.00 3.02
3329 6686 7.712264 TGCATGAAATTTTCTTAACCACTTG 57.288 32.000 10.33 0.00 0.00 3.16
3330 6687 9.643693 CTATGCATGAAATTTTCTTAACCACTT 57.356 29.630 10.16 0.00 0.00 3.16
3331 6688 7.761249 GCTATGCATGAAATTTTCTTAACCACT 59.239 33.333 10.16 0.00 0.00 4.00
3332 6689 7.761249 AGCTATGCATGAAATTTTCTTAACCAC 59.239 33.333 10.16 0.00 0.00 4.16
3333 6690 7.839907 AGCTATGCATGAAATTTTCTTAACCA 58.160 30.769 10.16 3.64 0.00 3.67
3335 6692 9.962759 CAAAGCTATGCATGAAATTTTCTTAAC 57.037 29.630 10.16 1.73 0.00 2.01
3336 6693 9.926158 TCAAAGCTATGCATGAAATTTTCTTAA 57.074 25.926 10.16 0.00 0.00 1.85
3337 6694 9.926158 TTCAAAGCTATGCATGAAATTTTCTTA 57.074 25.926 10.16 0.00 35.11 2.10
3338 6695 8.836268 TTCAAAGCTATGCATGAAATTTTCTT 57.164 26.923 10.16 1.51 35.11 2.52
3339 6696 7.548075 CCTTCAAAGCTATGCATGAAATTTTCT 59.452 33.333 10.16 0.00 36.66 2.52
3340 6697 7.332678 ACCTTCAAAGCTATGCATGAAATTTTC 59.667 33.333 10.16 2.05 36.66 2.29
3341 6698 7.163441 ACCTTCAAAGCTATGCATGAAATTTT 58.837 30.769 10.16 0.39 36.66 1.82
3342 6699 6.704310 ACCTTCAAAGCTATGCATGAAATTT 58.296 32.000 10.16 2.46 36.66 1.82
3343 6700 6.290294 ACCTTCAAAGCTATGCATGAAATT 57.710 33.333 10.16 0.00 36.66 1.82
3344 6701 5.927281 ACCTTCAAAGCTATGCATGAAAT 57.073 34.783 10.16 0.00 36.66 2.17
3357 6714 8.095169 AGTACTTGTATACTCCAACCTTCAAAG 58.905 37.037 4.17 0.00 28.86 2.77
3383 6740 1.000145 CGAGACGACGACTCATCAGA 59.000 55.000 23.31 0.00 34.47 3.27
3384 6741 0.722282 ACGAGACGACGACTCATCAG 59.278 55.000 23.31 11.79 37.03 2.90
3385 6742 1.136057 CAACGAGACGACGACTCATCA 60.136 52.381 23.31 0.00 37.03 3.07
3386 6743 1.128136 TCAACGAGACGACGACTCATC 59.872 52.381 23.31 1.49 37.03 2.92
3387 6744 1.154197 TCAACGAGACGACGACTCAT 58.846 50.000 23.31 8.96 37.03 2.90
3388 6745 1.128136 GATCAACGAGACGACGACTCA 59.872 52.381 23.31 7.65 37.03 3.41
3389 6746 1.128136 TGATCAACGAGACGACGACTC 59.872 52.381 15.88 15.88 37.03 3.36
3390 6747 1.128878 CTGATCAACGAGACGACGACT 59.871 52.381 0.00 0.00 37.03 4.18
3391 6748 1.136029 ACTGATCAACGAGACGACGAC 60.136 52.381 0.00 0.00 37.03 4.34
3392 6749 1.128136 GACTGATCAACGAGACGACGA 59.872 52.381 0.00 0.00 37.03 4.20
3393 6750 1.525596 GACTGATCAACGAGACGACG 58.474 55.000 0.00 0.00 39.31 5.12
3394 6751 1.469308 AGGACTGATCAACGAGACGAC 59.531 52.381 0.00 0.00 0.00 4.34
3395 6752 1.822506 AGGACTGATCAACGAGACGA 58.177 50.000 0.00 0.00 0.00 4.20
3396 6753 2.418976 TGTAGGACTGATCAACGAGACG 59.581 50.000 0.00 0.00 0.00 4.18
3397 6754 4.167268 GTTGTAGGACTGATCAACGAGAC 58.833 47.826 0.00 0.00 32.56 3.36
3398 6755 3.192844 GGTTGTAGGACTGATCAACGAGA 59.807 47.826 0.00 0.00 40.37 4.04
3399 6756 3.193691 AGGTTGTAGGACTGATCAACGAG 59.806 47.826 0.00 0.00 40.37 4.18
3411 6768 4.348461 TGGACACAATTACAGGTTGTAGGA 59.652 41.667 0.00 0.00 37.69 2.94
3414 6771 4.141459 TGGTGGACACAATTACAGGTTGTA 60.141 41.667 4.69 0.00 37.69 2.41
3446 6803 7.997107 TCATGAGGACGTAATATGTAACAAC 57.003 36.000 0.00 0.00 0.00 3.32
3447 6804 8.035984 TGTTCATGAGGACGTAATATGTAACAA 58.964 33.333 0.00 0.00 0.00 2.83
3448 6805 7.548967 TGTTCATGAGGACGTAATATGTAACA 58.451 34.615 0.00 2.63 0.00 2.41
3449 6806 7.705325 ACTGTTCATGAGGACGTAATATGTAAC 59.295 37.037 0.00 0.30 0.00 2.50
3450 6807 7.704899 CACTGTTCATGAGGACGTAATATGTAA 59.295 37.037 0.00 0.00 0.00 2.41
3451 6808 7.147966 ACACTGTTCATGAGGACGTAATATGTA 60.148 37.037 0.00 0.00 0.00 2.29
3459 6821 1.686587 TCACACTGTTCATGAGGACGT 59.313 47.619 0.00 0.00 0.00 4.34
3460 6822 2.438868 TCACACTGTTCATGAGGACG 57.561 50.000 0.00 0.00 0.00 4.79
3463 6825 4.155462 CCTTCAATCACACTGTTCATGAGG 59.845 45.833 0.00 0.00 0.00 3.86
3464 6826 4.379186 GCCTTCAATCACACTGTTCATGAG 60.379 45.833 0.00 0.00 0.00 2.90
3466 6828 3.366679 GGCCTTCAATCACACTGTTCATG 60.367 47.826 0.00 0.00 0.00 3.07
3475 6837 1.202915 TGCTCTTGGCCTTCAATCACA 60.203 47.619 3.32 0.00 40.92 3.58
3476 6838 1.538047 TGCTCTTGGCCTTCAATCAC 58.462 50.000 3.32 0.00 40.92 3.06
3487 6849 3.261580 TCATGTGAACGTATGCTCTTGG 58.738 45.455 0.00 0.00 0.00 3.61
3499 6861 4.925054 CACAACCAATGGAATCATGTGAAC 59.075 41.667 6.16 0.00 33.18 3.18
3512 6874 1.201954 CGATCACGAGCACAACCAATG 60.202 52.381 0.00 0.00 42.66 2.82
3534 6896 3.690475 TGAGTACTCAGTCACGGACTA 57.310 47.619 21.74 0.00 41.37 2.59
3548 6910 1.002087 CCAACCCAGTGTCCTGAGTAC 59.998 57.143 0.00 0.00 41.50 2.73
3551 6913 1.376466 CCCAACCCAGTGTCCTGAG 59.624 63.158 0.00 0.00 41.50 3.35
3573 6935 0.324943 CCACCGGACAAAGATCAGGT 59.675 55.000 9.46 0.00 46.67 4.00
3574 6936 1.026718 GCCACCGGACAAAGATCAGG 61.027 60.000 9.46 0.00 39.62 3.86
3588 6951 0.463116 CCCGGTAGTAACATGCCACC 60.463 60.000 0.00 0.00 0.00 4.61
3605 6968 1.337074 TGATCGAACACAACGGTACCC 60.337 52.381 6.25 0.00 0.00 3.69
3606 6969 1.723003 GTGATCGAACACAACGGTACC 59.277 52.381 19.68 0.16 40.11 3.34
3610 6973 1.779061 CGGTGATCGAACACAACGG 59.221 57.895 24.73 9.04 42.40 4.44
3651 7014 1.568504 TAACAGGGATCTTGCCGTCT 58.431 50.000 0.00 0.00 30.73 4.18
3657 7020 4.502259 CGGAGGAGATTAACAGGGATCTTG 60.502 50.000 0.00 0.00 32.96 3.02
3680 7043 1.380112 ACTCTCCTCAGCGGTACCC 60.380 63.158 6.25 0.00 0.00 3.69
3737 7100 5.222337 ACCACCTCTTCCATTGGTTTTATCT 60.222 40.000 1.86 0.00 39.41 1.98
3740 7103 4.148838 CACCACCTCTTCCATTGGTTTTA 58.851 43.478 1.86 0.00 40.51 1.52
3748 7111 0.119155 TCTCCCACCACCTCTTCCAT 59.881 55.000 0.00 0.00 0.00 3.41
3752 7115 0.119155 TCCATCTCCCACCACCTCTT 59.881 55.000 0.00 0.00 0.00 2.85
3755 7118 0.990282 CCATCCATCTCCCACCACCT 60.990 60.000 0.00 0.00 0.00 4.00
3756 7119 0.988145 TCCATCCATCTCCCACCACC 60.988 60.000 0.00 0.00 0.00 4.61
3758 7121 1.679981 TTTCCATCCATCTCCCACCA 58.320 50.000 0.00 0.00 0.00 4.17
3781 7144 0.958876 ACCCGGATTTTTCGTCTGGC 60.959 55.000 0.73 0.00 40.19 4.85
3785 7148 2.004733 CTGGTACCCGGATTTTTCGTC 58.995 52.381 10.07 0.00 29.82 4.20
3788 7151 1.100510 GCCTGGTACCCGGATTTTTC 58.899 55.000 25.39 3.22 29.82 2.29
3794 7157 0.031917 TTGATAGCCTGGTACCCGGA 60.032 55.000 25.39 6.38 29.82 5.14
3826 7189 4.100808 ACTGCATTGGAGGAATCTCTACTC 59.899 45.833 10.12 0.00 39.86 2.59
3827 7190 4.036518 ACTGCATTGGAGGAATCTCTACT 58.963 43.478 10.12 0.00 39.86 2.57
3828 7191 4.125703 CACTGCATTGGAGGAATCTCTAC 58.874 47.826 10.12 0.00 39.86 2.59
3829 7192 3.135348 CCACTGCATTGGAGGAATCTCTA 59.865 47.826 17.89 0.00 39.24 2.43
3830 7193 2.092538 CCACTGCATTGGAGGAATCTCT 60.093 50.000 17.89 0.00 39.24 3.10
3831 7194 2.295885 CCACTGCATTGGAGGAATCTC 58.704 52.381 17.89 0.00 39.24 2.75
3832 7195 1.684248 GCCACTGCATTGGAGGAATCT 60.684 52.381 26.07 0.00 39.24 2.40
3833 7196 0.743097 GCCACTGCATTGGAGGAATC 59.257 55.000 26.07 3.93 39.24 2.52
3842 7205 2.691526 CTGTATTGATGGCCACTGCATT 59.308 45.455 8.16 6.16 40.13 3.56
3919 7285 5.163663 GGAATCATCGTTGCTGATTTTGGTA 60.164 40.000 0.27 0.00 42.03 3.25
3930 7296 5.305585 TCTTTATAGGGGAATCATCGTTGC 58.694 41.667 0.00 0.00 0.00 4.17
3942 7308 4.713792 AGCTGGTGATTCTTTATAGGGG 57.286 45.455 0.00 0.00 0.00 4.79
3963 7329 6.496911 TGTCTCAGCTGCAGGGTTTATATATA 59.503 38.462 17.12 0.00 0.00 0.86
3964 7330 5.307976 TGTCTCAGCTGCAGGGTTTATATAT 59.692 40.000 17.12 0.00 0.00 0.86
3965 7331 4.653801 TGTCTCAGCTGCAGGGTTTATATA 59.346 41.667 17.12 0.00 0.00 0.86
3966 7332 3.455910 TGTCTCAGCTGCAGGGTTTATAT 59.544 43.478 17.12 0.00 0.00 0.86
3967 7333 2.837591 TGTCTCAGCTGCAGGGTTTATA 59.162 45.455 17.12 0.00 0.00 0.98
4100 7771 3.118738 ACCACACTTTCGTTCTCTTCTGT 60.119 43.478 0.00 0.00 0.00 3.41
4253 7928 4.689345 ACTTGGTGCTGTTATCTTACGAAC 59.311 41.667 0.00 0.00 0.00 3.95
4294 7969 6.516718 TCAAAATTAATTTGTTTGGCTCCGA 58.483 32.000 14.04 0.00 46.89 4.55
4295 7970 6.777526 TCAAAATTAATTTGTTTGGCTCCG 57.222 33.333 14.04 0.00 46.89 4.63
4296 7971 9.964303 AAATTCAAAATTAATTTGTTTGGCTCC 57.036 25.926 14.04 0.00 46.89 4.70
4353 8028 2.135139 TCATGAACGCTTATCATCGCC 58.865 47.619 0.00 0.00 35.38 5.54
4371 8047 6.597672 CACTATTACAGGTTTTGGCACTATCA 59.402 38.462 0.00 0.00 0.00 2.15
4373 8049 5.357032 GCACTATTACAGGTTTTGGCACTAT 59.643 40.000 0.00 0.00 0.00 2.12
4375 8051 3.506067 GCACTATTACAGGTTTTGGCACT 59.494 43.478 0.00 0.00 0.00 4.40
4401 8077 7.001099 AGCTATAGCCGGCTATTTAAAACTA 57.999 36.000 44.65 27.23 43.38 2.24
4402 8078 5.866207 AGCTATAGCCGGCTATTTAAAACT 58.134 37.500 44.65 29.88 43.38 2.66
4403 8079 5.121925 GGAGCTATAGCCGGCTATTTAAAAC 59.878 44.000 44.65 30.15 43.38 2.43
4404 8080 5.243207 GGAGCTATAGCCGGCTATTTAAAA 58.757 41.667 44.65 29.19 43.38 1.52
4405 8081 4.619863 CGGAGCTATAGCCGGCTATTTAAA 60.620 45.833 44.65 29.52 43.67 1.52
4406 8082 3.119245 CGGAGCTATAGCCGGCTATTTAA 60.119 47.826 44.65 29.85 43.67 1.52
4407 8083 2.426024 CGGAGCTATAGCCGGCTATTTA 59.574 50.000 44.65 30.51 43.67 1.40
4408 8084 1.204941 CGGAGCTATAGCCGGCTATTT 59.795 52.381 44.65 31.93 43.67 1.40
4409 8085 0.818296 CGGAGCTATAGCCGGCTATT 59.182 55.000 44.65 31.45 43.67 1.73
4410 8086 2.494677 CGGAGCTATAGCCGGCTAT 58.505 57.895 42.09 42.09 43.67 2.97
4411 8087 3.998156 CGGAGCTATAGCCGGCTA 58.002 61.111 36.88 36.88 43.67 3.93
4416 8092 2.028020 AGGCAATAACGGAGCTATAGCC 60.028 50.000 21.17 12.26 43.38 3.93
4417 8093 3.320673 AGGCAATAACGGAGCTATAGC 57.679 47.619 17.33 17.33 42.49 2.97
4418 8094 5.758296 TGAAAAGGCAATAACGGAGCTATAG 59.242 40.000 0.00 0.00 0.00 1.31
4419 8095 5.676552 TGAAAAGGCAATAACGGAGCTATA 58.323 37.500 0.00 0.00 0.00 1.31
4420 8096 4.523083 TGAAAAGGCAATAACGGAGCTAT 58.477 39.130 0.00 0.00 0.00 2.97
4421 8097 3.938963 CTGAAAAGGCAATAACGGAGCTA 59.061 43.478 0.00 0.00 0.00 3.32
4422 8098 2.749621 CTGAAAAGGCAATAACGGAGCT 59.250 45.455 0.00 0.00 0.00 4.09
4423 8099 2.488153 ACTGAAAAGGCAATAACGGAGC 59.512 45.455 0.00 0.00 0.00 4.70
4424 8100 5.163754 CCTTACTGAAAAGGCAATAACGGAG 60.164 44.000 0.00 0.00 39.69 4.63
4425 8101 4.698304 CCTTACTGAAAAGGCAATAACGGA 59.302 41.667 0.00 0.00 39.69 4.69
4426 8102 4.981794 CCTTACTGAAAAGGCAATAACGG 58.018 43.478 0.00 0.00 39.69 4.44
4436 8112 1.523758 AGCGGCACCTTACTGAAAAG 58.476 50.000 1.45 0.00 0.00 2.27
4437 8113 2.843401 TAGCGGCACCTTACTGAAAA 57.157 45.000 1.45 0.00 0.00 2.29
4438 8114 2.843401 TTAGCGGCACCTTACTGAAA 57.157 45.000 1.45 0.00 0.00 2.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.